ABSTRACT The objective of this project is to elucidate the regulatory mechanisms and biological significance of the epigenetic programming of the sex chromosomes in the male germline. During male meiosis, unsynapsed sex chromosomes are epigenetically silenced in a process called meiotic sex chromosome inactivation (MSCI), which is necessary for spermatogenesis. During the term of the previous grant, we elucidated the underlying mechanisms of MSCI and demonstrated the role of DNA damage response (DDR) factors as essential regulators. Establishment of MSCI requires phosphorylation of the histone variant H2AX (?H2AX) to spread from the axes to the chromosome-wide domain of the sex chromosomes. This process is directed by MDC1, a binding partner of ?H2AX, at the onset of the pachytene stage. Downstream of MDC1, SCML2, a germline- specific Polycomb protein, is recruited to ?H2AX-containing nucleosomes and required for epigenetic programming. During the last project period, we unexpectedly found that initiation of MSCI is tightly coupled to active DNA demethylation. Initially the DNA demethylation is directed by MDC1 and precedes the establishment of silent histone modifications. In this renewal application, we will test the central hypothesis that the DDR pathway regulates active DNA demethylation, enabling the epigenetic programming of sex chromosomes necessary for male reproduction. While DNA methylation is generally associated with gene silencing, we propose that DNA demethylation is linked to gene silencing in MSCI. Our data suggest that demethylation in MSCI involves two major phases: the initial phase is mediated by the DDR pathway at the early pachytene stage (Aim 1) and the later phase is mediated by SCML2 downstream of the DDR at the mid- pachytene stage (Aim 2). This study will establish a novel link between DDR signaling and active DNA demethylation, and will further elucidate the biological significance of the epigenetic programming of the sex chromosomes, which is essential for male reproduction.